4IN7

(M)L214N mutant of the Rhodobacter sphaeroides Reaction Center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Role of Rhodobacter sphaeroides photosynthetic reaction center residue M214 in the composition, absorbance properties, and conformations of H(A) and B(A) cofactors.

Saer, R.G.Hardjasa, A.Rosell, F.I.Mauk, A.G.Murphy, M.E.Beatty, J.T.

(2013) Biochemistry 52: 2206-2217

  • DOI: 10.1021/bi400207m
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsible for the dechelation of the central Mg(2+) of bacteriochlorophyll (BChl) was investigated by replacement of (M)214 with residues possessing small, nonpolar side chains that can neither coordinate nor block access to the central metal ion ...

    In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsible for the dechelation of the central Mg(2+) of bacteriochlorophyll (BChl) was investigated by replacement of (M)214 with residues possessing small, nonpolar side chains that can neither coordinate nor block access to the central metal ion. The (M)L214 side chain was also replaced with Cys, Gln, and Asn to evaluate further the requirements for assembly of the RC with BChl in the HA pocket. Photoheterotrophic growth studies showed no difference in growth rates of the (M)214 nonpolar mutants at a low light intensity, but the growth of the amide-containing mutants was impaired. The absorbance spectra of purified RCs indicated that although absorbance changes are associated with the nonpolar mutations, the nonpolar mutant RC pigment compositions are the same as in the wild-type protein. Crystal structures of the (M)L214G, (M)L214A, and (M)L214N mutants were determined (determined to 2.2-2.85 Å resolution), confirming the presence of BPhe in the HA pocket and revealing alternative conformations of the phytyl tail of the accessory BChl in the BA site of these nonpolar mutants. Our results demonstrate that (i) BChl is converted to BPhe in a manner independent of the aliphatic side chain length of nonpolar residues replacing (M)214, (ii) BChl replaces BPhe if residue (M)214 has an amide-bearing side chain, (iii) (M)214 side chains containing sulfur are not sufficient to bind BChl in the HA pocket, and (iv) the (M)214 side chain influences the conformation of the phytyl tail of the BA BChl.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein H chainH266Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein L chainL282Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein M chainM307Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download CCD File 
M
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
GGD
Query on GGD

Download CCD File 
H
NONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY] -1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER
C52 H94 O15
OGKQOSUHVSQNSH-IQXSWRQFSA-N
 Ligand Interaction
BCL
Query on BCL

Download CCD File 
L, M
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
BPH
Query on BPH

Download CCD File 
M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
U10
Query on U10

Download CCD File 
L, M
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
PC1
Query on PC1

Download CCD File 
M
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
SPO
Query on SPO

Download CCD File 
M
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
LDA
Query on LDA

Download CCD File 
L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

Download CCD File 
L
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
H, L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.138α = 90
b = 139.138β = 90
c = 185.14γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description